A novel hierarchical clustering algorithm for gene sequences

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Wei, Dan ^a,b   Jiang, Qingshan ^b   Wei, Yanjie ^b   Wang, Shengrui ^c  

^a XIAMEN UNIVERSITY   (China)

^b SHENZHEN INSTITUTES OF ADVANCED TECHNOLOGY   (China)

^c UNIVERSITÉ DE SHERBROOKE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT-FREE; BIOLOGICAL CHARACTERISTIC; CLUSTERING METHODS; DISTANCE MEASURE; FEATURE VECTORS; GENE SEQUENCES; HIERARCHICAL CLUSTERING ALGORITHMS; ORDER RELATION; PHYLOGENETIC ANALYSIS; SEQUENCE SIMILARITY;

BIOINFORMATICS; DNA SEQUENCES; FUNCTIONAL GROUPS;

CLUSTERING ALGORITHMS;

ALGORITHM; ARTICLE; BIOLOGY; CLUSTER ANALYSIS; COMPARATIVE STUDY; DNA SEQUENCE; METHODOLOGY; NUCLEOTIDE SEQUENCE; PHYLOGENY;

ALGORITHMS; BASE SEQUENCE; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

EID: 84866326775     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-174     Document Type: Article

References (58)

1. Demuth JP, De Bie T, Stajich JE, Cristianini N, Hahn MW. The evolution of mammalian gene families. PLoS One 2006, 1:1-10.
2. Zhao B, Duan V, Yau SS. A novel clustering method via nucleotide-based Fourier power spectrum analysis. JTheor Biol 2011, 279:83-89.
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. A basic local alignment search tool. JMol Biol 1990, 215:403-410.
4. Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. ProcNatlAcad Sci USA 1988, 85(8):2444-2488.
5. Vinga S, Almeida J. Alignment-free sequence comparison-a review. Bioinformatics 2003, 19(4):513-523. 10.1093/bioinformatics/btg005, 12611807.
6. Haubold B, Reed FA, Pfaffelhuber P. Alignment-free estimation of nucleotide diversity. Bioinformatics 2011, 27(4):449-455. 10.1093/bioinformatics/btq689, 21156730.
7. Liu Z, Meng J, Sun X. A novel feature-based method for whole genome phylogenetic analysis without alignment: application to HEV genotyping and subtyping. Biochem Biophys Res Commun 2008, 368(2):223-230. 10.1016/j.bbrc.2008.01.070, 18230342.
8. Domazet-Loso M, Haubold B. Efficient estimation of pairwise distances between genomes. Bioinformatics 2009, 25(24):3221-3227. 10.1093/bioinformatics/btp590, 19825795.
9. Domazet-Loso M, Haubold B. Alignment-free detection of local similarity among viral and bacterial genomes. Bioinformatics 2011, 27(11):1466-1472. 10.1093/bioinformatics/btr176, 21471011.
10. Kelil A, Wang S, Brzezinski R, Fleury A. CLUSS: Clustering of protein sequences based on a new similarity measure. BMC Bioinformatics 2007, 8:286. 10.1186/1471-2105-8-286, 1976428, 17683581.
11. Reinert G, Chew D, Sun FZ, Waterman MS. Alignment-free sequence comparison (I): statistics and power. JComput Biol 2009, 16(12):1615-1634.
12. Dai Q, Liu X, Yao Y, Zhao F. Numerical characteristics of word frequencies and their application to dissimilarity measure for sequence comparison. JTheor Biol 2011, 276(1):174-180.
13. Lu G, Zhang S, Fang X. An improved string composition method for sequence comparison. BMC Bioinformatics 2008, 9(Suppl 6):S15. 10.1186/1471-2105-9-S6-S15, 2638155, 19091014.
14. Aita T, Husimi Y, Nishigaki K. A mathematical consideration of the word-composition vector method in comparison of biological sequences. BioSystems 2011, 106:67-75. 10.1016/j.biosystems.2011.06.009, 21745534.
15. Blaisdell BE. A measure of the similarity of sets of sequences not requiring sequence alignment. ProcNatlAcad Sci USA 1986, 83:5155-5159.
16. Wu TJ, Burke JP, Davison DB. A measure of DNA sequence dissimilarity based on Mahalanobis distance between frequencies of words. Biometrics 1997, 53(4):1431-1439. 10.2307/2533509, 9423258.
17. Wu TJ, Hsieh YC, Li LA. Statistical measures of DNA dissimilarity under Markov chain models of base composition. Biometrics 2001, 57(2):441-448. 10.1111/j.0006-341X.2001.00441.x, 11414568.
18. Stuart GW, Moffett K, Baker S. Integrated gene and species phylogenies from unaligned whole genome protein sequences. Bioinformatics 2002, 18(1):100-108. 10.1093/bioinformatics/18.1.100, 11836217.
19. Fichant G, Gautier C. Statistical method for predicting protein coding regions in nucleic acid sequences. ComputAppl Biosci 1987, 3(4):287-295.
20. Wang J, Zheng X. WSE, a new sequence distance measure based on word frequencies. Math Biosci 2008, 215(1):78-83. 10.1016/j.mbs.2008.06.001, 18590747.
21. Zheng X, Qin Y, Wang J. A Poisson model of sequence comparison and its application to coronavirus phylogeny. Math Biosci 2009, 217(2):159-166. 10.1016/j.mbs.2008.11.006, 19073197.
22. Yang K, Zhang L. Performance comparison of gene family clustering methods with expect curated gene family data set in Arabidposis thaliana. Planta 2008, 228:439-447. 10.1007/s00425-008-0748-7, 18493791.
23. Dong G, Pei J. Classification, clustering, features and distances of sequence Data. Sequence Data Mining 2007, 33:47-65.
24. Sokal RR, Rohlf FJ. Biometry: The Principles and Practice of Statistics in Biological Research 1995, W. H. Freeman and Company, New York, 3.
25. Everitt BS, Landau S, Leese M. Cluster Analysis 2001, Oxford University Press, London.
26. Loewenstein Y, Portugaly E, Fromer M, Linial M. Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. Bioinformatics 2008, 24(13):i41-i49. 10.1093/bioinformatics/btn174, 2718652, 18586742.
27. National Center for Biotechnology Information (NCBI) Documentation of the BLASTCLUST-algorithm ftp://ftp.ncbi.nih.gov/blast/documents/blastclust.html, National Center for Biotechnology Information (NCBI).
28. Enright AJ, Ouzounis CA. GeneRAGE: a robust algorithm for sequence clustering and domain detection. Bioinformatics 2000, 16(5):451-457. 10.1093/bioinformatics/16.5.451, 10871267.
29. Chaudhuri P, Das S. SWORDS: A statistical tool for analyzing large DNA sequences. J Biosci 2002, 27(1):1-6. 10.1007/BF02703678, 11927772.
30. Uchiyama I. Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes. Nucleic Acids Res 2006, 34(2):647-658. 10.1093/nar/gkj448, 1351371, 16436801.
31. Hao X, Jiang R, Chen T. Clustering 16 S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. Bioinformatics 2011, 27(5):611-618. 10.1093/bioinformatics/btq725, 3042185, 21233169.
32. Sperisen P, Pagni M. JACOP: a simple and robust method for the automated classification of protein sequences with modular architecture. BMC Bioinformatics 2005, 6:216. 10.1186/1471-2105-6-216, 1208858, 16135248.
33. Wan X, Bridges SM, Boyle JA, Boyle AP. Interactive Clustering for Exploration of Genomic Data. SmartEng Design 2002, 12:753-758.
34. Kelarev A, Kang B, Steane D. Clustering Algorithms for ITS Sequence Data with Alignment Metrics. Lect Notes ComputSci 2006, 4304:1027-1031.
35. Tseng GC. Penalized and weighted K-means for clustering with scattered objects and prior information in high-throughput biological data. Bioinformatics 2007, 23(17):2247-2255. 10.1093/bioinformatics/btm320, 17597097.
36. Ashlock D, Warner E. Classifying Synthetic and Biological DNA Sequences with Side Effect Machines. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology: 15-17 Sept. 2008; Sun Valley, ID 2008, 22-29.
37. Zhao Y, Karypis G. Criterion functions for document clustering: experiments and analysis 2001, Technical Report.
38. Kashef R, Kamel MS. Enhanced bisecting k-means clustering using intermediate cooperation. Pattern Recognit 2009, 42(11):2557-2569.
39. Li W, Godzik A. Cd-hit: a Fast Program for Clustering and Comparing Large Sets of Protein or Nucleotide Sequences. Bioinformatics 2006, 22(13):1658-1659. 10.1093/bioinformatics/btl158, 16731699.
40. Alam I, Cornell M, Soanes DM, Hedeler C, Wong HM, Rattray M, Hubbard SJ, Talbot NJ, Oliver SG, Paton NW. A Methodology for Comparative Functional Genomics. JIntegr Bioinform 2007, 4(3):69.
41. Picardi E, Mignone F, Pesole G. EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data. BMC Bioinformatics 2009, 10(Suppl 6):S10. 10.1186/1471-2105-10-S6-S10, 2788350, 19958509.
42. Wei D, Jiang Q. A DNA Sequence Distance Measure Approach for Phylogenetic Tree Construction. 5th IEEE International Conference on Bio-Inspired Computing: Theories and Applications: 23-26 Sept. 2010 Changsha 2010, 204-212. Li K, Tang Z, Li R, Nagar AK, Thamburaj R.
43. Neumann-Held EM. The gene is dead-Long live the gene: Conceptualizing genes the constructionist way. Sociobiology and Bioeconomics: the Theory of Evolution in Biological and Economic Theory 1999, 105-137. Springer, Berlin, Koslowski P.
44. White JR, Navlakha S, Nagarajan N, Ghodsi M, Kingsford C, Pop M. Alignment and clustering of phylogenetic markers- implications for microbial diversity studies. BMC bioinformatics 2010, 11:152. 10.1186/1471-2105-11-152, 2859756, 20334679.
45. Waterman MS. Introduction to Computational Biology: Maps, Sequences, and Genomes 1995, Chapman and Hall, Lodon.
46. Durbin R, Eddy SR, Krogh A, Mitchison G. Biological Sequence Analysis: probabilistic models of proteins and nucleic acids 1998, Cambridge University Press, Cambridge.
47. Nair ASS, Mahalakshmi T. Visualization of genomic data using inter-nucleotide distance signals. Proceedings of IEEE Genomic Signal Processing: 11-13 July 2005; Bucharest 2005,
48. Schmitt AO, Herzel H. Estimating the Entropy of DNA sequences. JTheor Biol 1997, 188(3):369-377.
49. Li C, Wang J. Relative entropy of DNA and its application. Physica A: Stat Mech Appl 2005, 347:465-471.
50. Steinbach M, Karypis G, Kumar V. A comparison of document clustering techniques. KDD Workshop on Text Mining: 20-23 August 2000; Boston
51. Zhao Y, Karypis G. Hierarchical Clustering Algorithms for Document Datasets. Data Mining Knowl Discov 2005, 10:141-168.
52. Larsen B, Aone C. Fast and effective text mining using linear-time document clustering. Proceedings of the fifth ACM SIGKDD international conference on Knowledge discovery and data mining: 15-18 August 1999; San Diego 1999, 16-22. Fayyad U, Chaudhuri S, Madigan D.
53. Page RD. TreeView: an application to display phylogenetic trees on personal computers. Bioinformatics 1996, 12:357-358.
54. Feng J, Hu Y, Wan P, Zhang A, Zhao W. New method for comparing DNA primary sequences based on a discrimination measure. JTheor Biol 2010, 266(4):703-707.
55. Cao Y, Janke A, Waddell PJ, Westerman M, Takenaka O, Murata S, Okada N, Paabo S, Hasegawa M. Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders. JMol Evol 1998, 47(3):307-322.
56. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 2003, 31(13):3497-3500. 10.1093/nar/gkg500, 168907, 12824352.
57. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32(5):1792-1797. 10.1093/nar/gkh340, 390337, 15034147.
58. Zhao B, He RL, Yau SS. A new distribution vector and its application in genome clustering. MolPhylogenet Evol 2011, 59(2):438-443.